Diagnostic markers of acute encephalitis syndrome and COVID-associated multisystem inflammatory syndrome in children from Southern India.

Acute encephalitis syndrome (AES) in children poses a significant public health challenge in India. This study aims to explore the utility of host inflammatory mediators and neurofilament (NfL) levels in distinguishing etiologies, assessing disease severity, and predicting outcomes in AES. We assessed 12 mediators in serum (n = 58) and 11 in cerebrospinal fluid (CSF) (n = 42) from 62 children with AES due to scrub typhus, viral etiologies, and COVID-associated multisystem inflammatory syndrome (MIS-C) in Southern India. Additionally, NfL levels in serum (n = 20) and CSF (n = 18) were examined. Clinical data, including Glasgow coma scale (GCS) and Liverpool outcome scores, were recorded. Examining serum and CSF markers in the three AES etiology groups revealed notable distinctions, with scrub typhus differing significantly from viral and MIS-C causes. Viral causes had elevated serum CCL11 and CCL2 compared with scrub typhus, while MIS-C cases showed higher HGF levels than scrub typhus. However, CSF analysis showed a distinct pattern with the scrub typhus group exhibiting elevated levels of IL-1RA, IL-1ß, and TNF compared with MIS-C, and lower CCL2 levels compared with the viral group. Modeling the characteristic features, we identified that age ≥3 years with serum CCL11 < 180 pg/mL effectively distinguished scrub typhus from other AES causes. Elevated serum CCL11, HGF, and IL-6:IL-10 ratio were associated with poor outcomes (p = 0.038, 0.005, 0.02). Positive CSF and serum NfL correlation, and negative GCS and serum NfL correlation were observed. Median NfL levels were higher in children with abnormal admission GCS and poor outcomes. Measuring immune mediators and brain injury markers in AES provides valuable diagnostic insights, with the potential to facilitate rapid diagnosis and prognosis. The correlation between CSF and serum NfL, along with distinctive serum cytokine profiles across various etiologies, indicates the adequacy of blood samples alone for assessment and monitoring. The association of elevated levels of CCL11, HGF, and an increased IL-6:IL-10 ratio with adverse outcomes suggests promising avenues for therapeutic exploration, warranting further investigation.

Correction: Contact tracing of COVID-19 in Karnataka, India: Superspreading and determinants of infectiousness and symptomatic infection.

[This corrects the article DOI: 10.1371/journal.pone.0270789.].

An ultrastructural and genomic study on the SARS-CoV-2 variant B.1.210 circulating during the first wave of COVID-19 pandemic in India.

PURPOSE: The study aims to isolate and understand cytopathogenesis, ultrastructure, genomic characteristics and phylogenetic analysis of SARS-CoV-2 virus of B.1.210 lineage, that circulated in India during first wave of the pandemic. METHODS: Clinical specimen from an interstate traveller from Maharashtra to Karnataka, in May 2020, who was positive by RT PCR for SARS-CoV-2 infection was subjected to virus isolation and Whole Genome Sequencing. Vero cells were used to study cytopathogenesis and ultrastructural features by Transmission Electron Microscopy (TEM). Phylogenetic analysis of the whole genome sequences of several SARS-CoV-2 variants downloaded from GISAID was performed in comparison with the B.1.210 variant identified in this study. RESULTS: The virus was isolated in Vero cells and identified by immunofluorescence assay and RT PCR. The growth kinetics in infected Vero cells revealed a peak viral titre at 24 â€‹h post-infection. Ultrastructural studies revealed distinct morphological changes with accumulation of membrane-bound vesicles containing pleomorphic virions in the cytoplasm, with single or multiple intranuclear filamentous inclusions and dilated rough endoplasmic reticulum with viral particles. Whole genome sequence of the clinical specimen as well as the isolated virus revealed the virus to be of lineage B.1.210 with the D614G mutation in the spike protein. Phylogenetic analysis of the whole genome sequence in comparison with other variants reported globally revealed that the isolated SARS-CoV-2 virus of lineage B.1.210 is closely related to the original Wuhan virus reference sequence. CONCLUSIONS: The SARS-CoV-2 variant B.1.210 virus isolated here showed ultrastructural features and cytopathogenesis similar to that of the virus reported during early phase of pandemic. Phylogenetic analysis showed that the isolated virus is closely related to the original Wuhan virus, thereby suggesting that the SARS-CoV-2 lineage B.1.210 that was circulating in India during the early phase of pandemic is likely to have evolved from the original Wuhan strain.

Association of Scrub Typhus in Children with Acute Encephalitis Syndrome and Meningoencephalitis, Southern India.

Scrub typhus is an established cause of acute encephalitis syndrome (AES) in northern states of India. We systematically investigated 376 children with AES in southern India, using a stepwise diagnostic strategy for the causative agent of scrub typhus, Orientia tsutsugamushi, including IgM and PCR testing of blood and cerebrospinal fluid (CSF) to grade its association with AES. We diagnosed scrub typhus in 87 (23%) children; of those, association with AES was confirmed in 16 (18%) cases, probable in 55 (63%), and possible in 16 (18%). IgM detection in CSF had a sensitivity of 93% and specificity of 82% compared with PCR. Our findings suggest scrub typhus as an emerging common treatable cause of AES in children in southern India and highlight the importance of routine testing for scrub typhus in diagnostic algorithms. Our results also suggest the potential promise of IgM screening of CSF for diagnosis of AES resulting from scrub typhus.

A two-step process for in silico screening to assess the performance of qRTPCR kits against variant strains of SARS-CoV-2.

BACKGROUND: Since inception of the COVID-19 pandemic, early detection and isolation of positive cases is one of the key strategies to restrict disease transmission. Real time reverse transcription polymerase chain reaction (qRTPCR) has been the mainstay of diagnosis. Most of the qRTPCR kits were designed against the target genes of original strain of SARS-CoV-2. However, with the emergence of variant strains of SARS-CoV-2, sensitivity of the qRTPCR assays has reportedly reduced. In view of this, it is critical to continuously monitor the performance of the qRTPCR kits in the backdrop of variant strains of SARS-CoV-2. Real world monitoring of assay performance is challenging. Therefore, we developed a two-step in-silico screening process for evaluating the performance of various qRTPCR kits used in India. RESULTS: We analysed 73 qRT-PCR kits marketed in India, against the two SARS-CoV-2 VoCs. Sequences of both Delta (B.1.617.2) and Omicron (B.1.1.529) VoCs submitted to GISAID within a specific timeframe were downloaded, clustered to identify unique sequences and aligned with primer and probe sequences. Results were analysed following a two-step screening process. Out of 73 kits analysed, seven were unsatisfactory for detection of both Delta and Omicron VoCs, 10 were unsatisfactory for Delta VoC whereas 2 were unsatisfactory for only Omicron VoC. CONCLUSION: Overall, we have developed a useful screening process for evaluating the performance of qRTPCR assays against Delta and Omicron VoCs of SARS-CoV-2 which can be used for detecting SARS-CoV-2 VoCs that may emerge in future and can also be redeployed for other evolving pathogens of public health importance.

Impact of Antecedent Infections on the Antibodies against Gangliosides and Ganglioside Complexes in Guillain-Barré Syndrome: A Correlative Study.

Background and Aims: Guillain-Barré Syndrome (GBS), an immune-mediated neuropathy, is characterized by antibodies against gangliosides/ganglioside complexes (GSCs) of peripheral nerves. Antecedent infections have been reported to induce antibodies that cross-react with the host gangliosides and thereby have a pivotal role in conferring an increased risk for developing GBS. Data pertaining to the impact of various antecedent infections, particularly those prevalent in tropical countries like India on the ganglioside/GSC antibodies is sparse. We aimed at exploring the association between six antecedent infections and the profile of ganglioside/GSC antibodies in GBS. Methods: Patients with GBS (n = 150) and healthy controls (n = 50) were examined for the serum profile of antibodies against GM1, GM2, GD1a, GD1b, GT1b, and GQ1b and their GSCs by ELISA. These antibodies were correlated with immunoreactivities against Campylobacter jejuni, Japanese encephalitis (JE), dengue, influenza, zika, and chikungunya infections. Results: The frequencies of antibodies against six single gangliosides (P < 0.001) and their GSCs (P = 0.039) were significantly higher in patients as compared to controls. Except for GT1b-antibody which was more frequent in axonal GBS, none of the other ganglioside/GSC antibodies correlated with the electrophysiological subtypes of GBS. Antecedent JE infection was significantly associated with increased frequency of antibodies against GD1a, GD1b, GT1b, and GQ1b. Antibodies against GSCs were not influenced by the antecedent infections. Interpretation: This study for the first time shows an association between antecedent JE infection and ganglioside antibodies in GBS. This finding reinforces the determining role of antecedent infections on ganglioside antibody responses and the subsequent immunological processes in GBS.

Acid and Alkaline Phosphatases Specific activities and Expression as Biomarkers in Brain Tumor Grading and Correlation of Anaplastic Oligodendroglioma G-III to Meningiomas G-I among Brain Tumors and their primary culture.

BACKGROUND: Acid Phosphatase (ACP) and Alkaline Phosphatases (ALP) are hydrolases that remove phosphate groups from protein and nucleic acid respectively for regulation of cell function from ACP as lysosomal defence function and ALP membrane-bound as a barrier of the cell. The ACP and ALP-specific activities of Meningiomas (n = 75) and gliomas (n = 81) were compared among brain tumors, normal brain, and derived primary cell culture. METHODS: Total Protein and Phosphatases assays estimated by Spectrophotometer and Native PAGE Gel Electrophoresis. Brain tumor and primary explant lysosome studies were performed with an electron microscope. RESULTS: Average ACP specific activity exhibited 9.32617 ± 4.1144 for meningiomas (n = 55) and 5.91 ± 5.8305 for gliomas (n = 60) respectively as compared to normal brain 7.104 ± 1.33 (n = 120) nm/min/mg of protein. Average ALP exhibited 37.1862 ± 39.91 (n = 36) for meningiomas and 5.91 ± 5.83 (n = 60) for gliomas respectively as compared to normal brain (n = 117) 2.463 ± 1.01 nm/min/mg of protein. ACP and ALP exhibited higher activities for meningiomas but not for gliomas as compared to normal brain, in contrast, both expressed more activities in the majority of glioma cell lines and lower in meningioma cell lines. Interestingly gliomas exhibited similar average specific activities for ACP and ALP. While GBM IV exhibits lower ALP activities due to cell migration and higher ACP activity correlate too many storage lysosomes from Electron microscopic observation as compared to meningiomas. CONCLUSIONS: Higher ALP activities can be surrogate markers from meningiomas G-I, G-II to G-III respectively. However meningiomas G-III are similar to gliomas excluding Anaplastic Oligodendroglioma G- III which is similar to Meningiomas G-I even for cells growth patterns. Therefore, an ALP level in meningiomas indicates complementary diagnosis as antibody-ALP conjugates with anticancer drugs for efficiency in targeting brain tumor reduction.

Contact tracing of COVID-19 in Karnataka, India: Superspreading and determinants of infectiousness and symptomatic infection.

BACKGROUND: India has experienced the second largest outbreak of COVID-19 globally, yet there is a paucity of studies analysing contact tracing data in the region which can optimise public health interventions (PHI's). METHODS: We analysed contact tracing data from Karnataka, India between 9 March and 21 July 2020. We estimated metrics of transmission including the reproduction number (R), overdispersion (k), secondary attack rate (SAR), and serial interval. R and k were jointly estimated using a Bayesian Markov Chain Monte Carlo approach. We studied determinants of risk of further transmission and risk of being symptomatic using Poisson regression models. FINDINGS: Up to 21 July 2020, we found 111 index cases that crossed the super-spreading threshold of ≥8 secondary cases. Among 956 confirmed traced cases, 8.7% of index cases had 14.4% of contacts but caused 80% of all secondary cases. Among 16715 contacts, overall SAR was 3.6% [95% CI, 3.4-3.9] and symptomatic cases were more infectious than asymptomatic cases (SAR 7.7% vs 2.0%; aRR 3.63 [3.04-4.34]). As compared to infectors aged 19-44 years, children were less infectious (aRR 0.21 [0.07-0.66] for 0-5 years and 0.47 [0.32-0.68] for 6-18 years). Infectors who were confirmed ≥4 days after symptom onset were associated with higher infectiousness (aRR 3.01 [2.11-4.31]). As compared to asymptomatic cases, symptomatic cases were 8.16 [3.29-20.24] times more likely to cause symptomatic infection in their secondary cases. Serial interval had a mean of 5.4 [4.4-6.4] days, and case fatality rate was 2.5% [2.4-2.7] which increased with age. CONCLUSION: We found significant heterogeneity in the individual-level transmissibility of SARS-CoV-2 which could not be explained by the degree of heterogeneity in the underlying number of contacts. To strengthen contact tracing in over-dispersed outbreaks, testing and tracing delays should be minimised and retrospective contact tracing should be implemented. Targeted measures to reduce potential superspreading events should be implemented. Interventions aimed at children might have a relatively small impact on reducing transmission owing to their low symptomaticity and infectivity. We propose that symptomatic cases could cause a snowballing effect on clinical severity and infectiousness across transmission generations; further studies are needed to confirm this finding.

The role of SARS-CoV-2 genomic surveillance and innovative analytical platforms for informing public health preparedness in Bengaluru, India.

A comprehensive SARS-CoV-2 genomic surveillance programme that integrates logistics, laboratory work, bioinformatics, analytics, and timely reporting was deployed through a public-private partnership in the city of Bengaluru, Karnataka in India. As a result, 12461 samples have been sequenced and reported to the Karnataka State public health officials as time-sensitive, decision support during the last one year and uploaded in global public databases in a timely manner. This programme has developed an analytics platform for studying SARS-CoV-2 sequences and their epidemiological context. Continuous sequencing effort enabled timely detection of emergence of Omicron variant in India and the subsequent spread of the same and its sub-lineages with more logistic growth (BA.10, BA.12 and BA.5) in Bengaluru. Our data also helped to provide timely information on variants to determine which of the Variants of Concern tracked globally, were observed in Bengaluru, ensuring targeted efforts and reducing unwarranted fear. This effort highlights the importance of, and the urgent need to, increase genomic surveillance to support the states with limited sequencing and bioinformatics capacity. We describe the development and deployment of this end-to-end solution for genomic surveillance of SARS-CoV-2 in the city of Bengaluru.

An algorithmic approach to identifying the aetiology of acute encephalitis syndrome in India: results of a 4-year enhanced surveillance study.

BACKGROUND: Annual outbreaks of acute encephalitis syndrome pose a major health burden in India. Although Japanese encephalitis virus (JEV) accounts for around 15% of reported cases, the aetiology of most cases remains unknown. We aimed to establish an enhanced surveillance network and to use a standardised diagnostic algorithm to conduct a systematic evaluation of acute encephalitis syndrome in India. METHODS: In this large-scale, systematic surveillance study in India, patients presenting with acute encephalitis syndrome (ie, acute onset of fever with altered mental status, seizure, or both) to any of the 18 participating hospitals across Uttar Pradesh, West Bengal, and Assam were evaluated for JEV (serum and cerebrospinal fluid [CSF] IgM ELISA) per standard of care. In enhanced surveillance, JEV IgM-negative specimens were additionally evaluated for scrub typhus, dengue virus, and West Nile virus by serum IgM ELISA, and for Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, dengue virus, herpes simplex virus, and enterovirus by CSF PCR across five referral laboratories. In 2017, chikungunya and Leptospira serum IgM by ELISA and Zika virus serum and CSF by PCR were also tested. FINDINGS: Of 10 107 patients with acute encephalitis syndrome enrolled in enhanced surveillance between Jan 1, 2014, and Dec 31, 2017, 5734 (57·8%) of 9917 participants with available data were male and 6179 (62·7%) of 9856 were children aged 15 years and younger. Among patients who provided a sample of either CSF or serum in enhanced surveillance, an aetiology was identified in 1921 (33·2%) of 5786 patients enrolled between 2014 and 2016 and in 1484 (34·3%) of 4321 patients enrolled in 2017. The most commonly identified aetiologies were JEV (1023 [17·7%] of 5786 patients), scrub typhus (645 [18·5%] of 3489), and dengue virus (161 [5·2%] of 3124). Among participants who provided both CSF and serum specimens, an aetiology was identified in 1446 (38·3%) of 3774 patients enrolled between 2014 and 2016 and in 936 (40·3%) of 2324 enrolled in 2017, representing a 3·1-times increase in the number of patients with acute encephalitis syndrome with an identified aetiology compared with standard care alone (299 [12·9%]; p<0·0001). INTERPRETATION: Implementation of a systematic diagnostic algorithm in an enhanced surveillance platform resulted in a 3·1-times increase in identification of the aetiology of acute encephalitis syndrome, besides JEV alone, and highlighted the importance of scrub typhus and dengue virus as important infectious aetiologies in India. These findings have prompted revision of the national testing guidelines for this syndrome across India. FUNDING: US Centers for Disease Control and Prevention.

Infection of human microglial cell line CHME-3 to study neuropathogenesis of chikungunya virus.

Chikungunya virus (CHIKV) infection, generally characterised by fever, rash and debilitating polyarthralgia, and/or arthritis, also causes complications of the central nervous system, including encephalitis. However, the role of microglial cells in the neuropathogenesis of CHIKV is poorly understood. The current study characterised the progression of CHIKV infection in the human microglial cell line CHME-3. The susceptibility of these cells to CHIKV and the viral replication kinetics were assessed during the early and late phases of infection. The cell viability was determined using the cell viability assay. Ultrastructural changes in CHIKV infected CHME-3 cells were assessed using transmission electron microscopy. The results showed that CHME-3 cells are susceptible to CHIKV infection and support viral replication with no significant loss in cell viability until 72 h post infection. Ultrastructural studies revealed the formation of cytopathic vacuoles-I (CPV-I) in the early stages and CPV-II in later stages with several virions organized along the membrane of CPV-II. Profuse vacuolation was observed in the later stages of infection. Abnormal giant mitochondria with altered cristae were observed in infected cells with an electron-dense matrix. The study establishes CHME-3 cells as a potential model for investigating the role of human microglial cells in neuropathogenicity of CHIKV.

External quality assessment of COVID-19 real time reverse transcription PCR laboratories in India.

Sudden emergence and rapid spread of COVID-19 created an inevitable need for expansion of the COVID-19 laboratory testing network across the world. The strategy to test-track-treat was advocated for quick detection and containment of the disease. Being the second most populous country in the world, India was challenged to make COVID-19 testing available and accessible in all parts of the country. The molecular laboratory testing network was augmented expeditiously, and number of laboratories was increased from one in January 2020 to 2951 till mid-September, 2021. This rapid expansion warranted the need to have inbuilt systems of quality control/ quality assurance. In addition to the ongoing inter-laboratory quality control (ILQC), India implemented an External Quality Assurance Program (EQAP) with assistance from World Health Organization (WHO) and Royal College of Pathologists, Australasia. Out of the 953 open system rRTPCR laboratories in both public and private sector who participated in the first round of EQAP, 891(93.4%) laboratories obtained a passing score of > = 80%. The satisfactory performance of Indian COVID-19 testing laboratories has boosted the confidence of the public and policy makers in the quality of testing. ILQC and EQAP need to continue to ensure adherence of the testing laboratories to the desired quality standards.

COVID-19: a boon or a bane for the microbiologists.

BACKGROUND: In the situation where COVID-19 pandemic has placed unprecedented demands and pressure on the health care system, we wanted to analyze how the medical microbiologists of our country were affected. Was it actually an opportunity to showcase the specialty or was it a doom? A debate was organized as a key session in the national e-conference of the Indian Association of Medical Microbiologists, held on 10 December 2020. OBJECTIVES: The objective of the debate was to examine and analyze the various positive as well as negative impacts of COVID-19 on the discipline of the medical microbiology of our country. CONTENT: Before the debate a voting session was conducted to assess the opinion of the audience followed by a very interesting debate where both the speakers presented their view points. The points in favor of the discipline were, mainly up-gradation of the specialty of microbiology in terms of learning, skill development, infrastructure, networking & research opportunities related to COVID-19. While the main points against were, nerve wracking work load without much acknowledgement, performance pressure from hospital administration to maintain rapid turnaround time, and a forceful neglect of all other infectious diseases like tuberculosis and antimicrobial resistance which were the key battle fields of the medical microbiologists. Postgraduate & even undergraduate training programs got completely derailed to their disadvantage. By the end of the debate, it was concluded that COVID-19 was neither a boon nor a bane to the microbiologists. A balanced approach to the problem in hand is required without ignoring the pre-existing infectious diseases in our country. The post debate voting swayed the audience considerably for it to be a bane & the faculty debating for boon had a huge margin to begin with but finally won with a whisker indicating the intensity of the debate.

Second round statewide survey for estimation of the burden of active infection and anti-SARS-CoV-2 IgG antibodies in the general population of Karnataka, India

ObjectiveThe second round of the serial cross-sectional sentinel-based population survey to assess active infection, seroprevalence, and their evolution in the general population across Karnataka was conducted. Additionally, a longitudinal study among participants identified as COVID-19 positive in the first survey round was conducted to assess the clinical sensitivity of the testing kit used. MethodsThe cross-sectional study of 41,228 participants across 290 healthcare facilities in all 30 districts of Karnataka was done among three groups of participants (low, moderate, and high-risk). Consenting participants were subjected to real-time reverse transcription-polymerase chain reaction (RT-PCR) testing, and antibody (IgG) testing. ResultsOverall weighted adjusted seroprevalence of IgG was 15.6% (95% CI: 14.9-16.3), crude IgG prevalence was 15.0% and crude active prevalence was 0.5%. Statewide infection fatality rate (IFR) was estimated as 0.11%, and COVID-19 burden estimated between 26.1 to 37.7% (at 90% confidence). Clinical sensitivity of the IgG ELISA test kit was estimated as [≥]38.9%. ConclusionThe sentinel-based population survey helped identify districts that needed better testing, reporting, and clinical management. The state was far from attaining natural immunity during the survey and hence must step up vaccination coverage and enforce public health measures to prevent the spread of COVD-19.

Antecedent infections in Guillain-Barré syndrome patients from south India.

Guillain-Barré syndrome (GBS) is the commonest post-infectious inflammatory peripheral neuropathy with undiscerned aetiology. The commonly reported antecedent infections implicated in India include Campylobacter jejuni, chikungunya, dengue, and Japanese encephalitis (JE). In this study from south India, we investigated the role of these four agents in triggering GBS. This case-control study was performed on 150 treatment-naive patients with GBS and 150 age and sex-matched controls from the same community. IgM immunoreactivity for C. jejuni, chikungunya, and dengue was detected by enzyme-linked immunosorbent assay (ELISA) in serum of patients with GBS and control subjects. Immunoreactivity against JE was detected in serum as well as cerebrospinal fluid (CSF) from patients (n = 150) and orthopaedic control (n = 45) subjects. The immunoreactivity against infections was compared between demyelinating and axonal subtypes of GBS. Overall, 119/150 patients with GBS had serological evidence of antecedent infection. Amongst those with evidence of antecedent infection, 24 (16%), 8 (5%), and 9 (6%) patients were exclusively immunoreactive to chikungunya, JE, and C. jejuni, respectively. In the remaining patients (78/119), immunoreactivity to multiple pathogens was noted. Immunoreactivity to C. jejuni infection was found in 32% of GBS patients compared to 2.7% controls (P < .001), whereas to chikungunya virus was reported in 66.7% of patients with GBS compared to 44.7% controls (P = .006). Anti-dengue immunoreactivity was significantly associated with the demyelinating subtype of GBS. Patients positive for JE IgM (CSF) manifested demyelinating electrophysiology. In this large case-control study, immunoreactivity against multiple infectious agents was observed in a subset of patients. Chikungunya was the commonest antecedent infection, followed by C. jejuni.

Reduced T cell immunity in unmedicated, comorbidity-free obsessive-compulsive disorder: An immunophenotyping study.

BACKGROUND: Immune system aberrations have been postulated to play a role in the pathophysiology of Obsessive-compulsive disorder (OCD). This study was aimed to examine the profile of immune cell subsets in peripheral blood of un-medicated OCD patients. METHOD: Thirteen drug-naïve/free OCD patients and twenty-six age & sex matched healthy controls were recruited. Immunophenotyping was carried out by staining the whole blood specimens with fluorescent monoclonal antibodies against the cell surface markers such as CD45, CD3, CD16, CD56, CD8, CD4, CD28, CD25 and CD127, followed by data acquisition on BD FACSVerse™ flow cytometer. The proportions of CD4 and CD8 T cells; T regulatory (Tregs), Natural Killer (NK) cells and NK-T cells were compared between patients with OCD and healthy control subjects. RESULTS: Significantly reduced percentage of T regulatory (Treg) cells was observed in individuals with OCD compared to healthy control subjects [1.0 ± 0.7 vs. 1.9 ± 1.4; p = 0.03, r = 0.33]. CONCLUSION: Treg cells play a crucial role in regulating the immune response, especially by suppressing the functional activities of T cells. In this study, decreased population of Treg cells essentially indicates a dysregulated T cell and/or T cell mediated immune activation in drug-naïve OCD patients. This preliminary observation might form the basis of further studies examining the immuno-inflammatory/autoimmune origin of OCD.

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian State of Karnataka

As the pandemic of COVID-19 caused by the coronavirus SARS-CoV-2 continues, the selection of genomic variants which can influence how the pandemic progresses is of growing concern. Of particular concern, are those variants that carry mutations/amino acid changes conferring higher transmission, more severe disease, re-infection, and immune escape. These can broadly be classified as Variants of Concern (VOCs). VOCs have been reported from several parts of the world- UK (lineage B.1.1.7), South Africa (lineage B.1.351) and, Brazil (lineage P.1/B.1.1.28). The conditions that contribute to the emergence of VOCs are not well understood. International travel remains an important means of spread. To track importation, spread, and the emergence of variants locally; we sequenced whole genomes of SARS-CoV-2 from international travellers (n=75) entering Karnataka, a state in South India, between Dec 22, 2020- Jan 31, 2021, and from positive cases in the city of Bengaluru (n=108), between Nov 22, 2020- Jan 22, 2021. The resulting 176 SARS-CoV-2 genomes could be classified into 34 lineages, that were either imported (73/176) or circulating (103/176) in this time period. The lineage B.1.1.7 (a.k.a the UK variant) was the major lineage imported into the state (24/73, 32.9%), followed by B.1.36 (20/73, 27.4%) and B.1 (14/73, 19.2%). We identified B.1.36 (45/103; 43.7%), B.1 (26/103; 25.2%), B.1.1.74 (5/103; 4.9%) and B.1.468 (4/103; 3.9%) as the major variants circulating in Bengaluru city. A distinct clade within the B.1.36 lineage was associated with a local outbreak. Analysis of the complete genomes predicted multiple amino acid replacements in the Spike protein. In total, we identified nine amino acid changes (singly or in pairs) in the Receptor Binding Domain of the Spike protein. Of these, the amino acid replacement N440K was found in 37/65 (56.92%) sequences in the B.1.36 lineage. The E484K amino acid change which is present in both VOCs, B.1.351 and P.1/B.1.1.28, was found in a single circulating virus in the B.1.36 lineage. This study highlights the introduction of VOCs by travel and the local circulation of viruses with amino acid replacements in the Spike protein. These were spread across lineages, suggesting that multiple paths can lead to the emergence of VOCs, this, in turn, highlights the need to sequence and limit outbreaks of SARS-CoV-2 locally. Our data support the use of concentrated and continued genomic surveillance of SARS-CoV-2 to direct public health measures, suggest revisions to vaccines, and serve as an early warning system to prepare for a surge in COVID-19 cases.

Descriptive epidemiology of SARS-CoV-2 infection in Karnataka state, South India: Transmission dynamics of symptomatic vs. asymptomatic infections.

BACKGROUND: The huge surge in COVID-19 cases in Karnataka state, India, during early phase of the pandemic especially following return of residents from other states and countries required investigation with respect to transmission dynamics, clinical status, demographics, comorbidities and mortality. Knowledge on the role of symptomatic and asymptomatic cases in transmission of SARS-CoV-2 was not available. METHODS: The study included all the cases reported from March 8 - May 31, 2020. Individuals with a history of international or domestic travel from high burden states, Influenza-like Illness or Severe Acute Respiratory Illness and high-risk contacts of COVID-19 cases were included. Detailed analysis based on contact tracing data available from the line-list of state surveillance unit was performed using cluster network analysis software. FINDINGS: Amongst the 3404 COVID-19 positive cases, 3096 (91%) were asymptomatic while 308 (9%) were symptomatic. Majority of asymptomatic cases were in the age range of 16 and 45 years while symptomatic cases were between 31 and 65 years. Mortality rate was especially higher among middle-aged and elderly cases with co-morbidities, 34/38 (89·4%). Cluster network analysis of 822 cases indicated that the secondary attack rate, size of the cluster and superspreading events were higher when the source case was symptomatic as compared to an asymptomatic. INTERPRETATION: Our findings indicate that both asymptomatic and symptomatic SARS-CoV-2 cases transmit the infection, although symptomatic cases were the main driving force within the state during the beginning of the pandemic. Considering the large proportion of asymptomatic cases, their ability to spread infection cannot be overlooked. Notwithstanding the limitations and bias in identifying asymptomatic cases, the findings have major implications for testing policies. Active search, early testing and treatment of symptomatic elderly patients with comorbidities should be prioritized for containing the spread of COVID-19 and reducing mortality. FUNDING: Intermediate Fellowship, Wellcome Trust-DBT India Alliance to Giridhara R Babu, Grant number: IA/CPHI/14/1/501499.

Epidemiology of SARS-CoV-2 infection in Karnataka State, South India: Transmission dynamics of symptomatic vs. asymptomatic infections

Background: In this report, we describe the epidemiology of SARS-CoV-2 infection, specifically examining how the symptomatic persons drove the transmission in the state of Karnataka, India, during the lockdown phase. Methods: The study included all the cases reported from March 8 to May 31, 2020 in the state. Any person with history of international or domestic travel from high burden states, those presenting with Influenza-like or Severe Acute Respiratory Illness and high-risk contacts of COVID19 cases, who were SARS-CoV-2 RT-PCR positive were included. Detailed analysis based on contact tracing data available from line-list of the state surveillance unit was performed using cluster analysis software package. Findings: Amongst the 3404 COVID-19 positive cases, 3096 (91%) were asymptomatic while 308 (9%) were symptomatic. Majority of the asymptomatic cases were in the age range of 16-50 years while symptomatic cases were between 31-65 years. Most of those affected were males. Cluster analysis of 822 cases indicated that the secondary attack rate, size of the cluster (dispersion) and occurrence of overt clinical illness is significantly higher when the index case in a cluster was symptomatic compared to an asymptomatic. Interpretation: Our findings indicate that both asymptomatic and symptomatic SARS-CoV-2 cases transmit the infection; however, the main driving force behind the spread of infection within the state was significantly higher from symptomatic cases. This has major implications for policies related to testing. Active search for symptomatic cases, subjecting them to testing and treatment should be prioritized for containing the spread of COVID-19.

Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka

An earlier version of this manuscript was removed owing to inclusion of confidential information relating to an individual